failed for URL: "whatsapp://" - error: This app is not allowed to query for scheme whatsapp

In iOS 9 you must whitelist any URL schemes your App wants to query in Info.plist under the LSApplicationQueriesSchemes key (an array of strings):

With the schemes included in Info.plist everything works as before. When you link against iOS 9 you are not limited to 50 distinct schemes you just need to declare what you need in Info.plist. There seems to be no limit for how many schemes you can include but I would expect questions from the App Store review team if they think you are abusing the mechanism.

Note that this mechanism only applies to canOpenURL and not openURL.
You do not need to have a scheme listed in Info.plist to be able to
open it with openURL.